Classification of the human THAP protein family identifies an evolutionarily conserved coiled coil region

Abstract

Background: The THAP (Thanatos Associated Proteins) protein family in humans is implicated in various important cellular processes like epigenetic regulation, maintenance of pluripotency, transposition and disorders like cancers and hemophilia. The human THAP protein family which consists of twelve members of different lengths has a well characterized amino terminal, zinc-coordinating, DNA-binding domain called the THAP domain. However, the carboxy terminus of most THAP proteins is yet to be structurally characterized. A coiled coil region is known to help in protein oligomerization in THAP1 and THAP11. It is not known if other human THAP proteins oligomerize. We have used bioinformatic tools to explore the possibility of dimerization of THAP proteins via a coiled coil region.

Results: Classification of human THAP protein into three size based groups led to the identification of an evolutionarily conserved alpha helical region, downstream of the amino terminal THAP domain. Secondary structure predictions, alpha helical wheel plots and protein models demonstrated the strong possibility of coiled coil formation in this conserved, leucine rich region of all THAP proteins except THAP10.

Conclusions: The identification of a predicted oligomerization region in the human THAP protein family opens new directions to investigate the members of this protein family.

Keywords: Classification; Leucine zipper; Oligomerization; THAP proteins.

Fig. 1

Multiple sequence alignment of leucine-rich alpha helical regions of human THAP proteins. The leucine rich alpha helical regions in human THAP proteins align with each other within THAP protein groups. a Helical region corresponds to residues143–188 (THAP1), 135–178 (THAP2), 189–224 (THAP3) and 148–193 (THAP6) (b) Helical region corresponds to residues 237–281 (THAP7), 180–209 (THAP8) and 254–310 (THAP11) (c) Helical region corresponds to residues 150–180 (THAP0), 362–398 (THAP4), 331–372 (THAP5) and 145–182 (THAP9). Boundaries of each protein are labelled. The Multiple Sequence Alignments were generated using CLUSTAL OMEGA and visualized using Jalview [47]. The color coding in Jalview is as follows; If each column has more than 60% hydrophobic amino acid residues, it is represented by blue, red represents more than 60% positively charged amino acid residues combined or more than 80% of either of the positively charged amino acid residues, more than 60% of negatively charged amino acid residues are represented by magenta, around 50 to 60% of polar amino acid residues are represented by green, Cysteine amino acid is pink colored, Glycine amino acid is orange colored, Proline amino acid is represented by yellow, more than 60% of aromatic amino acid residues are colored cyan and unconserved amino acid residues are represented as white

Fig. 2

Classification of the human THAP protein family. The human THAP protein family is classified into three groups; Short THAP proteins include THAP1, THAP2, THAP 3 and THAP 6, Medium sized THAP proteins include THAP7, THAP 8, THAP 10 and THAP 11 and Long THAP proteins include THAP0, THAP 4, THAP 5 and THAP 9. Boundaries of each protein are labelled, grey box represents the THAP domain and black box represents the evolutionarily conserved coiled coil region, which has been predicted in this study

Fig. 3

Prediction of secondary structure of THAP proteins. Predicted alpha helical regions are (a) sTHAP protein group: residues 143–188 (THAP1), 135–178 (THAP2), 189–224 (THAP3) and 148–193 (THAP6) (b) mTHAP protein group: residues 237–281 (THAP7), 180–209 (THAP8) and 254–310 (THAP11) (c) lTHAP protein group: residues 150–180 (THAP0), 362–398 (THAP4), 331–372 (THAP5) and 145–182 (THAP9). The secondary structure predicted by JPRED assigns a score from 0 to 9 for a predicted helix forming region, 0 being the lowest and 9 being the highest probability of forming a helix. The Heptad pattern is as described in Additional file 1: Figure S1a

Fig. 4

Group-wise protein residue conservation of predicted alpha helical region. a sTHAP protein group: THAP1, THAP2, THAP3 and THAP6 (b) mTHAP protein group: THAP7, THAP8, and THAP11 (c) lTHAP protein: THAP0, THAP5, and THAP9. The graph shows the conservation probability of each amino acid residue

Fig. 5

Superposition of the predicted alpha helical region of sTHAP protein group. The predicted alpha helical regions of sTHAP group proteins; THAP1 (143–188), THAP2 (135–180), THAP3 (180–225) and THAP6 (148–193) were represented as cartoon within the rest of each protein represented as ribbon and superposed using VMD. Green represents THAP1 protein, blue represent THAP2 protein, red represents THAP3 protein and yellow represents THAP6 protein

Fig. 6

Helical wheel plot representation and electrostatic interactions predicted by DRAW COIL (a) sTHAP protein group: THAP1, THAP2, THAP3 and THAP6 (b) mTHAP protein group: THAP7, THAP8, and THAP11 (c) lTHAP protein: THAP0, THAP5, and THAP9. Helical wheel plots show the arrangement of amino acid residues in a heptad pattern. Non-polar residues are colored grey, polar residues are colored yellow, acidic residues are colored red and basic residues are colored blue. The red dotted lines represent electrostatic repulsive interactions and the blue dotted lines represent electrostatic attractive interactions